I just finished the game but the end was pretty strange and confusing..

Spoiler below!

So apparently I wasn't able to save Agrippa. I gathered all the ingredients and just wandered around not knowing what to do with them. So I randomly entered the chancel and the monsters struck me down and I woke up in the cell. When I came back to Agrippa the laboratory was open, so I went in and tried to mix Agrippa's potion. I placed the poison gland and bone in the instruments, but I couldn't use the glass jar on them.. It just said "I can't do this right now" or something. I couldn't figure out what was wrong, and after a while I just went to the chancel again and I was able to enter the inner sanctum, where I tore down the stone rods and apparently killed Alexander. I don't know what happened to Agrippa, did I do something wrong? Are the several endings to the game?

You first have to distill the blood, then you have to put the glass jar under the apparatus for the mushroom and extract the poison from the mushroom and finally use the jar at the bone extractor.

There are 3 endings:
Good one: Use Agrippa's head on the portal when it opens
Bad one: Don't do anything in the chamber, just let Alexander go through the portal
Revenge one: Smash the pillars before the portal opens to kill Alexander

You first have to distill the blood, then you have to put the glass jar under the apparatus for the mushroom and extract the poison from the mushroom and finally use the jar at the bone extractor.

There are 3 endings:
Good one: Use Agrippa's head on the portal when it opens
Bad one: Don't do anything in the chamber, just let Alexander go through the portal
Revenge one: Smash the pillars before the portal opens to kill Alexander

Hello! I suggest looking up a guide on either the Steam forums, GameFAQs, or perhaps even YouTube for the answer to your question. You've bumped a really old thread, which is okay, but the persons in this thread are long gone and will be unable to answer your question. Please open a new thread and ask your question there